5Y58 | pdb_00005y58

Crystal structure of Ku70/80 and TLC1

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Ku	e5y58A1	A: beta barrels	X: SPOC domain-like	H: SPOC domain-related	T: Ku70/80 subunit middle domain	F: Ku	ECOD (1.6)
A	Ku_N	e5y58A2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: Ku_N	ECOD (1.6)
D [auth C]	Ku	e5y58C1	A: beta barrels	X: SPOC domain-like	H: SPOC domain-related	T: Ku70/80 subunit middle domain	F: Ku	ECOD (1.6)
D [auth C]	Ku_N	e5y58C2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: Ku_N	ECOD (1.6)
G [auth E]	Ku	e5y58E1	A: beta barrels	X: SPOC domain-like	H: SPOC domain-related	T: Ku70/80 subunit middle domain	F: Ku	ECOD (1.6)
G [auth E]	Ku_N	e5y58E2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: Ku_N	ECOD (1.6)
B	Ku	e5y58B1	A: beta barrels	X: SPOC domain-like	H: SPOC domain-related	T: Ku70/80 subunit middle domain	F: Ku	ECOD (1.6)
B	Ku_N	e5y58B2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: Ku_N	ECOD (1.6)
E [auth D]	Ku	e5y58D1	A: beta barrels	X: SPOC domain-like	H: SPOC domain-related	T: Ku70/80 subunit middle domain	F: Ku	ECOD (1.6)
E [auth D]	Ku_N	e5y58D2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: Ku_N	ECOD (1.6)
H [auth F]	Ku	e5y58F1	A: beta barrels	X: SPOC domain-like	H: SPOC domain-related	T: Ku70/80 subunit middle domain	F: Ku	ECOD (1.6)
H [auth F]	Ku_N	e5y58F2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: Ku_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (utative)
D [auth C]	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (utative)
G [auth E]	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (utative)
B	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (utative)
E [auth D]	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (utative)
H [auth F]	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth C], G [auth E]	PF02735	Ku70/Ku80 beta-barrel domain (Ku)	Ku70/Ku80 beta-barrel domain	The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-bi ...	The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-binding beta-barrel domain. This domain is found in both the Ku70 Swiss:P12956 and Ku80 Swiss:P13010 proteins that form a DNA binding heterodimer [1].	Domain
A, D [auth C], G [auth E]	PF03730	Ku70/Ku80 C-terminal arm (Ku_C)	Ku70/Ku80 C-terminal arm	-	Family
A, D [auth C], G [auth E]	PF03731	Ku70/Ku80 N-terminal alpha/beta domain (Ku_N)	Ku70/Ku80 N-terminal alpha/beta domain	The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal ...	The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold [1].	Domain
B, E [auth D], H [auth F]	PF02735	Ku70/Ku80 beta-barrel domain (Ku)	Ku70/Ku80 beta-barrel domain	The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-bi ...	The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-binding beta-barrel domain. This domain is found in both the Ku70 Swiss:P12956 and Ku80 Swiss:P13010 proteins that form a DNA binding heterodimer [1].	Domain
B, E [auth D], H [auth F]	PF03731	Ku70/Ku80 N-terminal alpha/beta domain (Ku_N)	Ku70/Ku80 N-terminal alpha/beta domain	The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal ...	The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth C], G [auth E]	ATP-dependent DNA helicase II subunit 1	ATP-dependent activity, acting on DNA nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid helicase activity catalytic activity macromolecular conformation isomerase activity ATP-dependent activity sequence-specific DNA binding DNA binding binding nucleic acid binding ATP-dependent activity, acting on DNA nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid helicase activity catalytic activity macromolecular conformation isomerase activity ATP-dependent activity sequence-specific DNA binding DNA binding binding nucleic acid binding telomeric DNA binding damaged DNA binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding RNA binding telomerase RNA binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides	regulation of cellular process negative regulation of biological process cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of cellular process negative regulation of biological process cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process silent mating-type cassette heterochromatin formation negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process double-strand break repair via break-induced replication nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair telomere organization chromosome organization telomere maintenance organelle organization localization establishment of protein-containing complex localization to telomere macromolecule localization establishment of localization subtelomeric heterochromatin formation mitochondrial double-strand break repair mitochondrial double-strand break repair via homologous recombination double-strand break repair via nonhomologous end joining	membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system protein-containing complex nuclear protein-containing complex Ku70:Ku80 complex membraneless organelle membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system protein-containing complex nuclear protein-containing complex Ku70:Ku80 complex membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region
B, E [auth D], H [auth F]	ATP-dependent DNA helicase II subunit 2	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity RNA binding telomerase RNA binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides sequence-specific DNA binding telomeric DNA binding damaged DNA binding	localization protein localization to chromosome protein localization to organelle macromolecule localization intracellular protein localization establishment of protein-containing complex localization to telomere establishment of localization cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process localization protein localization to chromosome protein localization to organelle macromolecule localization intracellular protein localization establishment of protein-containing complex localization to telomere establishment of localization cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process cellular process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair subtelomeric heterochromatin formation regulation of cellular process negative regulation of biological process cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process regulation of metabolic process developmental process sex determination cellular developmental process reproductive process mating type determination reproductive process in single-celled organism donor selection developmental process involved in reproduction mating type switching double-strand break repair via nonhomologous end joining telomere organization chromosome organization telomere maintenance organelle organization	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex Ku70:Ku80 complex intracellular membrane-bounded organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex Ku70:Ku80 complex intracellular membrane-bounded organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region
C [auth X], F [auth Y], I [auth Z]	TLC1	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth C], G [auth E]	IPR016194	SPOC-like, C-terminal domain superfamily	Homologous Superfamily
A, D [auth C], G [auth E]	IPR005161	Ku70/Ku80, N-terminal alpha/beta	Domain
A, D [auth C], G [auth E]	IPR006164	Ku70/Ku80, DNA-binding domain	Domain
A, D [auth C], G [auth E]	IPR047087	Ku70, core domain	Domain
A, D [auth C], G [auth E]	IPR005160	Ku70/Ku80 C-terminal arm	Domain
A, D [auth C], G [auth E]	IPR006165	Ku70	Family
A, D [auth C], G [auth E]	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
B, E [auth D], H [auth F]	IPR024193	Ku80	Family
B, E [auth D], H [auth F]	IPR016194	SPOC-like, C-terminal domain superfamily	Homologous Superfamily
B, E [auth D], H [auth F]	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
B, E [auth D], H [auth F]	IPR005161	Ku70/Ku80, N-terminal alpha/beta	Domain
B, E [auth D], H [auth F]	IPR006164	Ku70/Ku80, DNA-binding domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.